If you're in Europe, the Cybook e-readers have drag and drop folder style of organization. None of the big manufacturers have this functionality, bizarrely. Turn the wifi off. If you know what you're doing, you could pick up a Nook Simple Touch and root it then you can do what you want with it.

There's no need to root the Nook ST. You can just drag and drop files and folders into the My Files/Books folder. Then just choose the "My Files" option to view your books and you'll see your Folders.